Fifteen of the top 20 state salaries in 2012 worked at SUNY Downstate Medical Center, the financially strapped Brooklyn facility that was criticized for mismanagement in a comptroller’s audit last month.

The top earner in the state was Antonio Alfonso, a professor at the center and its head of surgery. He earned nearly $1.1 million last year through his various roles. He ranked second in 2011 at $776,000.

SUNY officials said the salaries of their top doctors are largely funded through clinical income, not taxpayer money.

Union officials were quick to point out that the high salaries are far from the norm. The average union worker in state government earns about $40,000 a year, they said.

“The vast majority of jobs in state service don’t pay even close to six figures,” said Stephen Madarasz, spokesman for the Civil Service Employees Association, the state’s largest public workers’ union.

“Unfortunately, the public has a lot of misconceptions about high-priced public employees because of a lot of highly visible, political patronage in the upper echelons,” he continued.

Ranked second on the list was Alain Kaloyeros, vice president and chief administrative officer of the College of Nanoscale Science and Engineering at SUNY Albany. He earned $797,391 last year after ranking first on the list in 2011. In 2011, he made $792,582.

Kaloyeros also received $559,039 in 2011 from research grants through the SUNY Research Foundation, the college said. The 2012 figure was not yet available.

Nearly 1,500 employees earned more money than Cuomo’s $179,000 salary in 2012. That’s up 33 percent from 2010, a report last month from the Empire Center for New York State Policy said.

In his proposed budget last month, Cuomo said the number of positions in the state agencies he controls has dropped 14 percent since 2008, from 137,680 to 118,878.

“Under Governor Cuomo’s leadership, executive agency spending has decreased, bureaucracy has been consolidated and state government has been streamlined,” said Cuomo spokesman Richard Azzopardi.

SUNY Chancellor Nancy Zimpher’s reported income in 2012 jumped from nearly $490,000 in 2011 to $686,000 last year. The increase was due largely to back payments owed for her retirement benefits when she was hired in 2009, said spokesman David Doyle.

Her salary is $490,000, plus an annual retirement benefit of $55,400.

“The chancellor’s compensation is a matter of public record and was agreed to when she was hired by the Board of Trustees in 2009,” Doyle said.

SUNY Binghamton President Harvey Stenger earned $425,332 last year. His salary is $385,000, and he receives a $60,000 annual housing allowance, a college spokesman said, although the entire amount was not yet accounted for in the comptroller’s report.

Most of the high earners worked for State Police, which had been without a new class of recruits for three years before 2012. Last year, about 14 percent of the state employees earning more than $100,000 were employed by the agency, about 3,800 officers.

Some of the income was for overtime as State Police dealt with staffing shortages, said Thomas Mungeer, president of the State Troopers Police Benevolent Association.

There have been several new recruiting classes in recent months, but Mungeer said they are still down about 300 officers compared to a few years ago. Also, he said, 17 troopers have been killed in the line of duty since 2000. The union has about 3,500 members.

“It’s a tough job to qualify for, and you want the most qualified people to do it,” Mungeer said.